read-tree -m -u: avoid getting confused by intermediate symlinks.

read-tree -m -u: avoid getting confused by intermediate symlinks.

When switching from a branch with both x86_64/boot/Makefile and
i386/boot/Makefile to another branch that has x86_64/boot as a
symlink pointing at ../i386/boot, the code incorrectly removed
i386/boot/Makefile.

This was because we first removed everything under x86_64/boot
to make room to create a symbolic link x86_64/boot, then removed
x86_64/boot/Makefile which no longer exists but now is pointing
at i386/boot/Makefile, thanks to the symlink we just created.

This fixes it by using the has_symlink_leading_path() function
introduced previously for git-apply in the checkout codepath.
Earlier, "git checkout" was broken in t4122 test due to this
bug, and the test had an extra "git reset --hard" as a
workaround, which is removed because it is not needed anymore.

Signed-off-by: Junio C Hamano <junkio@cox.net>